Keep EquivalentTo axioms and pair text changes (#2)

[ubyndr]

Closes #2 (consumer half).

Two gaps found while working out why CLARA reviewed almost nothing on cell-ontology#3717.

equivalent_class kept its axiom

parse.py matched an equivalence axiom and then discarded it, returning kind="equivalent_class" with value, predicate_iri and value_label all None — so the agent could only emit "the equivalent-class axiom requires support".

ROBOT's markdown diff already renders these in Manchester syntax; the labels just arrive wrapped in markdown links. Stripping the links leaves a bare axiom:

buccal mucosa cell EquivalentTo keratinocyte and (part of some mouth mucosa)

text_deltas() — pairing removed/added text axioms

An OWL axiom's identity includes its annotations, so attaching one dbxref to an untouched definition is reported by ROBOT as a removed/added pair, indistinguishable from a rewrite. text_deltas() pairs the two sides per term and classifies each revised / refs_only / added / removed. extract.py emits it in changes.json for the router.

Without this, routing existing-term prose would re-verify unchanged definitions against their entire ref list on every ref-only edit.

Agent instructions

• New text_revision and refs_added routes. refs_added verifies the existing prose against the delta refs only — the pre-existing refs were justified when they landed.
• EquivalentTo asserts necessary and sufficient conditions, so both directions are now required as separate core assertions, with an explicit instruction not to pass the sufficient direction on evidence that only supports the necessary one. That direction is the one literature rarely states and the one that would otherwise pass silently.

Testing

New fixture 3717-buccal-mucosa-cell-edits, generated with ROBOT from the exact commits the CLARA run reviewed (d7ff69b9 → 51ef2001). It reproduces that run's routing summary: 12 reviewable, 7 decomposable.

39 tests pass, up from 28. The new assertions were mutation-checked — reverting either fix fails them:

test_3717_equivalent_class_carries_manchester_axiom   FAILED (axiom discarded)
test_3717_ref_only_def_edit_is_not_a_revision         FAILED (pairing removed)

Merge order

Land this before cell-ontology#3720. The router tolerates payloads without text_deltas, so either order is safe, but this one activates nothing on its own.

🤖 Generated with Claude Code

[ubyndr]

Ran the stage-2/3 agent against the routing this PR produces for cell-ontology#3717 — full reports below, also recorded in runs/CL_0000312, runs/CL_0002170, runs/CL_0002336.

All three land on term-level UNCERTAIN, but for three distinct, correctly-diagnosed reasons rather than the old "axiom discarded" dead end. Stage C (full-text escalation) is blocked repo-wide by #5, independent of this PR.

CL:0000312 — keratinocyte (refs_added) — 5 pass · 0 fail · 7 uncertain

Verifies the delta ref (PMID:21316034) only, per the new route — 5/12 assertions pass directly off it (oral AMP expression); the rest are pre-existing prose the new ref was never meant to cover.

Stage B ran against Asta snippet_search, scoped by paper_ids. Stage C (get_europepmc_full_text) returned empty output for every identifier tried (see issue #5), so unresolved core assertions could not be escalated to full text.

Routed targets

target_id	route	refs in scope	where those refs come from
refs_added:CL:0000312:1	refs_added	PMID:21316034	refs newly attached to the definition by this PR (delta only)

Assertions

#	Assertion	Cat	Verdict
a1	Keratinocytes are epithelial cells of stratified squamous tissues.	core	uncertain
a2	Keratinocytes are present in skin.	core	pass
a3	Keratinocytes are present in oral mucosa.	core	pass
a4	Keratinocytes are present in esophagus.	core	uncertain
a5	Keratinocytes produce keratin proteins.	core	uncertain
a6	Keratinocytes secrete antimicrobial peptides.	core	pass
a7	Keratinocytes form a barrier against environmental damage.	core	uncertain
a8	Keratinocytes form a barrier against dehydration.	core	uncertain
a9	Keratinocytes form a barrier against pathogens and microbial invasion.	core	pass
a10	Keratinocytes undergo successive stages of differentiation marked by changes in keratin expression.	core	uncertain
a11	Keratinocyte differentiation supports tissue integrity and wound repair.	core	uncertain
a12	Keratinocytes contribute to immune defense.	core	pass

Supporting evidence

a2, a3, a6, a9, a12 — PMID:21316034:

In the oral cavity, mucosal keratinocytes resist bacterial infection, in part, by producing broad-spectrum antimicrobial peptides (AMPs) including defensin, adrenomedullin and calprotectin... HGKs from three subjects expressed eleven AMPs, including S100A7, S100A8, S100A9, S100A12, secretory leukocyte protease inhibitor, lipocalin 2 (LCN2), cystatin C and β-defensin 2.

Unresolved: a1, a4, a5, a7, a8, a11 — no snippet in the new ref addresses these claims. a10 — snippet says IL-1α regulates cell differentiation, but nothing about keratin-marked stages.

CL:0002170 — keratinized cell of the oral mucosa (text_revision) — 0 pass · 0 fail · 3 uncertain

Correctly scoped to PMID:12014572, but that ref is inEPMC=N and absent from Asta, so all 3 assertions land uncertain — a retrieval gap, not a routing bug.

Routed targets

target_id	route	refs in scope	where those refs come from
text_revision:CL:0002170:1	text_revision	PMID:12014572	refs on the revised definition axiom

Assertions

#	Assertion	Cat	Verdict
a1	A keratinized cell of the oral mucosa is a keratinized buccal mucosa cell.	core	uncertain
a2	Keratinized cells of the oral mucosa are mostly located in the hard palate.	core	uncertain
a3	Keratinized cells of the oral mucosa are mostly located in the gingiva.	core	uncertain

Unresolved (not retrievable, 3): snippet_search returned 0 hits because PMID:12014572 is absent from the Asta corpus, and the paper is inEPMC=N so Stage C can't reach it either. The reference was in scope but could not be read.

CL:0002336 — buccal mucosa cell (text_revision + equivalent_class) — 0 pass · 0 fail · 4 uncertain (core)

The EquivalentTo axiom now survives (buccal mucosa cell EquivalentTo keratinocyte and (part of some mouth mucosa)) and is split into NECESSARY/SUFFICIENT assertions as designed, but the definition only carries GOC:tfm/MESH:D009061 — no searchable ref exists, so both directions are uncited.

Definition xrefs at head: GOC:tfm, MESH:D009061 — searchable: none

Assertions

#	Assertion	Cat	Verdict
a1	Buccal mucosa cells are epithelial cells.	core	uncertain
a2	Buccal mucosa cells line the oral cavity, including the mucosa of the gums, palate, lip and cheek.	core	uncertain
a3	The term 'buccal mucosa cell' is sometimes used only for the lining of the cheeks, as part of the lining mucosa.	background	uncertain
a4	NECESSARY: Every buccal mucosa cell is a keratinocyte that is part of the mouth mucosa.	core	uncertain
a5	SUFFICIENT: Every keratinocyte that is part of the mouth mucosa is a buccal mucosa cell.	core	uncertain

Unresolved (uncited, all 5): no PMID:/DOI: id on the definition axiom to search against; the comment's only xref is a Scielo URL, not an accepted id format.

cc @dosumis